Sampler has never accurately imported EXS and Kontakt loop points/x-fades (and probably other formats as well). Even when the sample points are identical to the source format, there is always a pop on looping unless the loop has been rendered in the audio file.
It seems that by manually adjusting the loop x-fade to 3 samples the problem is solved. Not a huge deal, but it's taken me 3 years to have this revelation!
